Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004102.1 Kokia drynarioides strain JFW-HI SEQ_117274, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 148655
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:178 original size:14 final size:14
Alignment explanation
Indices: 159--209 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
149 GATTTGACCC
*
159 GACCGTTGTCCATT
1 GACCGTTGACCATT
*
173 GACCGTTGACAATT
1 GACCGTTGACCATT
* *
187 GACTGTTGACCATC
1 GACCGTTGACCATT
*
201 GACAGTTGA
1 GACCGTTGA
210 TCGTTGACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (14 bp):
GACCGTTGACCATT
Found at i:204 original size:21 final size:21
Alignment explanation
Indices: 171--217 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
161 CCGTTGTCCA
* *
171 TTGACCGTTGACAATTGA-CTG
1 TTGACCATCGACAATTGATC-G
*
192 TTGACCATCGACAGTTGATCG
1 TTGACCATCGACAATTGATCG
213 TTGAC
1 TTGAC
218 TTTTTTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (21 bp):
TTGACCATCGACAATTGATCG
Found at i:2569 original size:3 final size:3
Alignment explanation
Indices: 2554--2590 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2544 TGGGAAAAAT
* *
2554 ATA ATA GTA ATA ATA ATT ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2591 AACTTGTGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:6757 original size:21 final size:21
Alignment explanation
Indices: 6731--6803 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
6721 GATTTGACCC
* * *
6731 GACCGTTGATCGTAGACAGTT
1 GACCGTTGACCATTGACAGTT
6752 GACCGTTGACCATTGACAGTT
1 GACCGTTGACCATTGACAGTT
**
6773 GACTATTGACCATTGACAGTT
1 GACCGTTGACCATTGACAGTT
*
6794 GATCGTTGAC
1 GACCGTTGAC
6804 TTTTTTCAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
GACCGTTGACCATTGACAGTT
Found at i:6761 original size:7 final size:7
Alignment explanation
Indices: 6731--6803 Score: 56
Period size: 7 Copynumber: 10.4 Consensus size: 7
6721 GATTTGACCC
6731 GACCGTT
1 GACCGTT
* *
6738 GATCGTA
1 GACCGTT
*
6745 GACAGTT
1 GACCGTT
6752 GACCGTT
1 GACCGTT
*
6759 GACCATT
1 GACCGTT
*
6766 GACAGTT
1 GACCGTT
**
6773 GACTATT
1 GACCGTT
*
6780 GACCATT
1 GACCGTT
*
6787 GACAGTT
1 GACCGTT
*
6794 GATCGTT
1 GACCGTT
6801 GAC
1 GAC
6804 TTTTTTCAAA
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (7 bp):
GACCGTT
Found at i:10225 original size:12 final size:12
Alignment explanation
Indices: 10208--10243 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
10198 TTTAAAGAGT
10208 ATAAAATAAAAG
1 ATAAAATAAAAG
*
10220 ATAAAATAAAAC
1 ATAAAATAAAAG
*
10232 AGAAAATAAAAG
1 ATAAAATAAAAG
10244 CAAAAGTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:14921 original size:11 final size:11
Alignment explanation
Indices: 14873--14922 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
14863 ATAACAATAT
14873 TTTTTTTTCTTC
1 TTTTTTTT-TTC
14885 TTTTCTTTTTTC
1 TTTT-TTTTTTC
*
14897 -TTTCTTTTTC
1 TTTTTTTTTTC
14907 TTTTTTTTTTC
1 TTTTTTTTTTC
14918 TTTTT
1 TTTTT
14923 CAAGTGACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 6 0.18
11 17 0.50
12 7 0.21
13 4 0.12
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:14922 original size:17 final size:17
Alignment explanation
Indices: 14872--14923 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 17
14862 TATAACAATA
14872 TTTTTTTTTCTTCTTTTCT
1 TTTTTTTTTC-T-TTTTCT
*
14891 TTTTTCTTTCTTTTTCT
1 TTTTTTTTTCTTTTTCT
14908 TTTTTTTTTCTTTTTC
1 TTTTTTTTTCTTTTTC
14924 AAGTGACTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 21 0.68
18 1 0.03
19 9 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTCTTTTTCT
Found at i:16019 original size:18 final size:19
Alignment explanation
Indices: 15970--16019 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
15960 CGGTAGGTTC
15970 CTTC-ATTTCATTC-TCAT
1 CTTCTATTTCATTCTTCAT
*
15987 CTTCTATTTCTTTCTTC-T
1 CTTCTATTTCATTCTTCAT
16005 CTTCT-TCTTCATTCT
1 CTTCTAT-TTCATTCT
16020 CCTTTTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 21 0.75
19 2 0.07
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (19 bp):
CTTCTATTTCATTCTTCAT
Found at i:32355 original size:53 final size:53
Alignment explanation
Indices: 32275--32380 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
32265 TATTTGTTTT
32275 GGGATTAGTCAACATTGTTGTTTGGGGGAGGGAATGTCTGAACTGTATTAATC
1 GGGATTAGTCAACATTGTTGTTTGGGGGAGGGAATGTCTGAACTGTATTAATC
*
32328 GGGATTAGTCAACATTGTTGTTTGGGGGAGGGAATTTCTGAACTGTATTAATC
1 GGGATTAGTCAACATTGTTGTTTGGGGGAGGGAATGTCTGAACTGTATTAATC
32381 ATTGTGTTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.25, C:0.09, G:0.31, T:0.35
Consensus pattern (53 bp):
GGGATTAGTCAACATTGTTGTTTGGGGGAGGGAATGTCTGAACTGTATTAATC
Found at i:35010 original size:36 final size:36
Alignment explanation
Indices: 34970--35040 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
34960 TTTGACTAGT
34970 TAATTCGGTTTTAATCGAACTATGAACACCCCTACC
1 TAATTCGGTTTTAATCGAACTATGAACACCCCTACC
*
35006 TAATTCGGTTTTAATCGAACTATGAACACTCCTAC
1 TAATTCGGTTTTAATCGAACTATGAACACCCCTAC
35041 ACTTCTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.32
Consensus pattern (36 bp):
TAATTCGGTTTTAATCGAACTATGAACACCCCTACC
Found at i:35754 original size:47 final size:47
Alignment explanation
Indices: 35697--35791 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
35687 AAGATAGAGC
35697 TATATCGCATCTAATCTATGACAAGTGGGACTCAATGATAGAAAAAA
1 TATATCGCATCTAATCTATGACAAGTGGGACTCAATGATAGAAAAAA
35744 TATATCGCATCTAATCTATGACAAGTGGGACTCAATGATAGAAAAAA
1 TATATCGCATCTAATCTATGACAAGTGGGACTCAATGATAGAAAAAA
35791 T
1 T
35792 TAAGGAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (47 bp):
TATATCGCATCTAATCTATGACAAGTGGGACTCAATGATAGAAAAAA
Found at i:37626 original size:12 final size:12
Alignment explanation
Indices: 37611--37650 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
37601 AACACTCTCC
37611 CTTCTCTTTTCT
1 CTTCTCTTTTCT
37623 CTTCTCTTTTC-
1 CTTCTCTTTTCT
37634 CTTCCTCTTTTCT
1 CTT-CTCTTTTCT
37647 CTTC
1 CTTC
37651 CTTGTGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
CTTCTCTTTTCT
Found at i:40285 original size:22 final size:20
Alignment explanation
Indices: 40251--40292 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
40241 TCTAGTCATA
40251 TAATAAATTATTATTATAAT
1 TAATAAATTATTATTATAAT
*
40271 TAATATAATTGATTATTTTAAT
1 TAATA-AATT-ATTATTATAAT
40293 AAATTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATAAATTATTATTATAAT
Found at i:40294 original size:25 final size:23
Alignment explanation
Indices: 40248--40318 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 23
40238 TTATCTAGTC
*
40248 ATATAATAAATTATTATT-ATAATT
1 ATATAAT-TATTATT-TTAATAATT
40272 AATATAATTGATTATTTTAATAAATT
1 -ATATAATT-ATTATTTTAAT-AATT
*
40298 ATTTAA-TATTATTTTAATAAT
1 ATATAATTATTATTTTAATAAT
40319 AAATTTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 3 0.07
23 11 0.27
24 3 0.07
25 20 0.49
26 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATATAATTATTATTTTAATAATT
Found at i:40331 original size:26 final size:26
Alignment explanation
Indices: 40289--40338 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40279 TTGATTATTT
* *
40289 TAATAAATTATTTAATATTATTTTAA
1 TAATAAATTATTAAATAATATTTTAA
40315 TAATAAATT-TTAAAATAATATTTT
1 TAATAAATTATT-AAATAATATTTT
40339 TCACATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATAAATTATTAAATAATATTTTAA
Found at i:40883 original size:18 final size:17
Alignment explanation
Indices: 40856--40896 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
40846 CAAATATAAA
*
40856 AAAAATTATTTTTTTTT
1 AAAAATTATTATTTTTT
40873 AAAAATATATTATTTTTT
1 AAAAAT-TATTATTTTTT
40891 AAAAAT
1 AAAAAT
40897 CAATTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAAATTATTATTTTTT
Found at i:40884 original size:21 final size:20
Alignment explanation
Indices: 40852--40890 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
40842 CATCCAAATA
40852 TAAAAAAAATTATTTTTTTT
1 TAAAAAAAATTATTTTTTTT
*
40872 TAAAAATATATTATTTTTT
1 TAAAAA-AAATTATTTTTT
40891 AAAAATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAAAAAAATTATTTTTTTT
Found at i:52752 original size:41 final size:41
Alignment explanation
Indices: 52688--52800 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 41
52678 TTGTAAAAAT
* * * *
52688 GGAAGACTCATGACTCG-GAATGAGCATGTGATTATGAATAA
1 GGAAGACTCATGTCTTGAG-ATGAGAATGAGATTATGAATAA
*
52729 GGAAGACTCATGTCTTGAGATGAGAATGAGATTATGATTAA
1 GGAAGACTCATGTCTTGAGATGAGAATGAGATTATGAATAA
* *
52770 GGAAGATTCATGTCTTTAGATGAGAATGAGA
1 GGAAGACTCATGTCTTGAGATGAGAATGAGA
52801 ATTTGGTTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
41 63 0.98
42 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (41 bp):
GGAAGACTCATGTCTTGAGATGAGAATGAGATTATGAATAA
Found at i:66905 original size:14 final size:14
Alignment explanation
Indices: 66882--66915 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
66872 TGTTTGACAG
66882 AAAATG-TTTCCGA
1 AAAATGATTTCCGA
*
66895 AAAATGATTTCTGA
1 AAAATGATTTCCGA
66909 AAAATGA
1 AAAATGA
66916 GTTACTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (14 bp):
AAAATGATTTCCGA
Found at i:83788 original size:21 final size:21
Alignment explanation
Indices: 83748--83797 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
83738 TCAGCATACT
* *
83748 CAGATGCATCCACAACAAAGG
1 CAGATGCAGCCACAACAAAGC
* *
83769 CAGATGCAGCCGCAATAAAGC
1 CAGATGCAGCCACAACAAAGC
*
83790 CAAATGCA
1 CAGATGCA
83798 CTCATATCAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.28, G:0.20, T:0.10
Consensus pattern (21 bp):
CAGATGCAGCCACAACAAAGC
Found at i:86613 original size:37 final size:37
Alignment explanation
Indices: 86542--86625 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 37
86532 TTATTACTAA
* * **
86542 TGTCGCTGCATGAGCACTTCTAGATTGCGTCCAAAAC
1 TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAC
* * *
86579 TGTCGTCGCATGAGCACTTCCAGATTTCACCCAAAAT
1 TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAC
86616 TGTCGCCGCA
1 TGTCGCCGCA
86626 GGAATATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (37 bp):
TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAC
Found at i:86776 original size:26 final size:26
Alignment explanation
Indices: 86726--86780 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
86716 CACCCAGGAA
*
86726 TGTCGCTGCATGAACATGGCCAGAAT
1 TGTCGCTGCATGAACATCGCCAGAAT
* * *
86752 TGTCGCTGCATGAACGTCTCTAGAAT
1 TGTCGCTGCATGAACATCGCCAGAAT
86778 TGT
1 TGT
86781 GCCTAGGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (26 bp):
TGTCGCTGCATGAACATCGCCAGAAT
Found at i:96675 original size:15 final size:15
Alignment explanation
Indices: 96657--96696 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
96647 TCTTAGTAGA
96657 TTCTTTCTCAGCATC
1 TTCTTTCTCAGCATC
* *
96672 TTCTTTCTTAGCGTC
1 TTCTTTCTCAGCATC
*
96687 TTCTTCCTCA
1 TTCTTTCTCA
96697 TCCTTTTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.10, C:0.33, G:0.07, T:0.50
Consensus pattern (15 bp):
TTCTTTCTCAGCATC
Found at i:114727 original size:21 final size:21
Alignment explanation
Indices: 114689--114728 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
114679 GGTTGACTCC
*
114689 AAGGACAAGAAAAGAAAGAGG
1 AAGGACAAGAAAAAAAAGAGG
114710 AAGGACAA-AAAGAAAAAGA
1 AAGGACAAGAAA-AAAAAGA
114729 AGCATAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.68, C:0.05, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGGACAAGAAAAAAAAGAGG
Found at i:121221 original size:18 final size:17
Alignment explanation
Indices: 121177--121221 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
121167 CAACAATTCG
121177 ACTCGACCTGTTGACCA
1 ACTCGACCTGTTGACCA
* *
121194 ACCCAAACCTGTTGACCAA
1 ACTC-GACCTGTTGACC-A
121213 ACTCGACCT
1 ACTCGACCT
121222 AGACTGTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.29, C:0.38, G:0.13, T:0.20
Consensus pattern (17 bp):
ACTCGACCTGTTGACCA
Found at i:121235 original size:7 final size:7
Alignment explanation
Indices: 121223--121267 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
121213 ACTCGACCTA
121223 GACTGTT
1 GACTGTT
121230 GACTGTT
1 GACTGTT
121237 GACTGTT
1 GACTGTT
*
121244 GACTATT
1 GACTGTT
*
121251 GACCGTT
1 GACTGTT
*
121258 GACCGTT
1 GACTGTT
121265 GAC
1 GAC
121268 GTTTTTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (7 bp):
GACTGTT
Found at i:128314 original size:27 final size:29
Alignment explanation
Indices: 128260--128315 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
128250 CAACCTAATA
128260 ACCCTAAGCCCAAATTTAACCAAACCCAAC
1 ACCCTAAG-CCAAATTTAACCAAACCCAAC
*
128290 ACCCTAAG-CAAA-TTAACCAAGCCCAA
1 ACCCTAAGCCAAATTTAACCAAACCCAA
128316 TTGGTCTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 4 0.16
30 8 0.32
ACGTcount: A:0.45, C:0.38, G:0.05, T:0.12
Consensus pattern (29 bp):
ACCCTAAGCCAAATTTAACCAAACCCAAC
Found at i:129651 original size:18 final size:19
Alignment explanation
Indices: 129622--129657 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
129612 TTAATTCAAA
129622 TTATAGATTATATATATAG
1 TTATAGATTATATATATAG
129641 TTATA-ATTATATATATA
1 TTATAGATTATATATATA
129658 AATATGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
TTATAGATTATATATATAG
Found at i:132252 original size:13 final size:13
Alignment explanation
Indices: 132234--132258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
132224 TAATGGCTTC
132234 AGAAATTTACTTT
1 AGAAATTTACTTT
132247 AGAAATTTACTT
1 AGAAATTTACTT
132259 GTAATGGACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
AGAAATTTACTTT
Found at i:136195 original size:13 final size:13
Alignment explanation
Indices: 136177--136210 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
136167 CCCCCTTATG
136177 GAAATTTCGTCCC
1 GAAATTTCGTCCC
136190 GAAATTTCGTCCC
1 GAAATTTCGTCCC
136203 GAAATTTC
1 GAAATTTC
136211 TTACTAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (13 bp):
GAAATTTCGTCCC
Found at i:145481 original size:34 final size:35
Alignment explanation
Indices: 145401--145506 Score: 103
Period size: 34 Copynumber: 3.1 Consensus size: 35
145391 CAATGATATT
* *
145401 AAATGTGAGCCTAACTCTAGTTGG-TAAACCAACG
1 AAATGTGAGCCCAACTCTAGTCGGATAAACCAACG
*
145435 ATAAT-TGCGCCCAACTCTAGTCGGATAAACCAAC-
1 A-AATGTGAGCCCAACTCTAGTCGGATAAACCAACG
* * * * *
145469 AAATGTGTGCCCAGCACTAGTCAGAT-AACTAACG
1 AAATGTGAGCCCAACTCTAGTCGGATAAACCAACG
145503 AAAT
1 AAAT
145507 AAATAATGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
33 9 0.15
34 39 0.65
35 12 0.20
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (35 bp):
AAATGTGAGCCCAACTCTAGTCGGATAAACCAACG
Found at i:145539 original size:108 final size:110
Alignment explanation
Indices: 145406--145655 Score: 337
Period size: 108 Copynumber: 2.3 Consensus size: 110
145396 ATATTAAATG
* *
145406 TGAGCCTAACTCTAGTTGG-TAAACCAACGATAATTGCGCCCAACT-CTAGTCGGATAAACCAAC
1 TGAGCCTAACTCTAGTTGGATAAACCAACGATAATTACGCCC-ACTGCTAGTCAGATAAACCAAC
145469 AAATGTGTGCCCAGCACTAGTCAGAT-AACTAACGAAAT-AAATAA
65 AAATGTGTGCCCAGCACTAGTCAGATAAACTAACGAAATGAAATAA
* * * * * * *
145513 TGAGCCCAACTCTAGTTGGATTAACCAACAATAATTATGCCCAGTGCTAGTCAGATAAATCGACA
1 TGAGCCTAACTCTAGTTGGATAAACCAACGATAATTACGCCCACTGCTAGTCAGATAAACCAACA
* * *
145578 AATGTGTGTCCAGCACTAGTCAGATAAACTGATGAAATGAAATAA
66 AATGTGTGCCCAGCACTAGTCAGATAAACTAACGAAATGAAATAA
**
145623 TGAGCCTGGCTCTAGTTGGATAAACCAACGATA
1 TGAGCCTAACTCTAGTTGGATAAACCAACGATA
145656 TTAATAATTA
Statistics
Matches: 122, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
107 20 0.16
108 58 0.48
109 10 0.08
110 34 0.28
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.23
Consensus pattern (110 bp):
TGAGCCTAACTCTAGTTGGATAAACCAACGATAATTACGCCCACTGCTAGTCAGATAAACCAACA
AATGTGTGCCCAGCACTAGTCAGATAAACTAACGAAATGAAATAA
Found at i:148486 original size:16 final size:16
Alignment explanation
Indices: 148435--148490 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
148425 AGCAAATAAT
*
148435 AATAAGAAATAACACAA
1 AATAA-AAATAAAACAA
* *
148452 TAATAATAATAACTA-AA
1 -AATAAAAATAA-AACAA
148469 AATAAAAATAAAACAA
1 AATAAAAATAAAACAA
148485 AATAAA
1 AATAAA
148491 TGATAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 1 0.03
16 18 0.56
17 7 0.22
18 6 0.19
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (16 bp):
AATAAAAATAAAACAA
Found at i:148577 original size:20 final size:20
Alignment explanation
Indices: 148467--148585 Score: 71
Period size: 20 Copynumber: 5.7 Consensus size: 20
148457 ATAATAACTA
*
148467 AAAATAAAAATAAAACAAAAT
1 AAAATAAAAAT-AAATAAAAT
* *
148488 AAATGATAATAATGATAGTAAAAT
1 AAA--ATAAAAAT-A-AATAAAAT
* *
148512 AAAACAACGAAT-AATAAAAT
1 AAAATAA-AAATAAATAAAAT
* * * *
148532 TAAATTAAATTAAAT-TAAT
1 AAAATAAAAATAAATAAAAT
*
148551 ACTAATAAAAATAAATAAAAT
1 A-AAATAAAAATAAATAAAAT
148572 AAAATAAAAATAAA
1 AAAATAAAAATAAA
148586 AGAATTTAAA
Statistics
Matches: 72, Mismatches: 19, Indels: 15
0.68 0.18 0.14
Matches are distributed among these distances:
19 5 0.07
20 37 0.51
21 7 0.10
22 3 0.04
23 11 0.15
24 9 0.12
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (20 bp):
AAAATAAAAATAAATAAAAT
Done.